where
model_map is the desired mapping of species,
reaction_compounds_final.csv is the entire network,
extracellular.txt is a manual mapping which compounds are in extracellular-space,
testmodel.txt is the output model

I am a biotechnologist with main focus on theoretical studies. Currently, I am working on the implementation of a parameter estimation algorithm on GPUs to reduce the computational burden of huge ODE systems.
I am a PAL and I am looking forward to communication with other SYSMO members.